I have added two GPUs, but BOINC only uses one

By default BOINC only uses the best GPU if more than one of the same brand is found. The best being decided by (decreasing priority):

Nvidia

• compute capability
  
• software version
  
• available memory
  
• speed
  

AMD

• double precision support
• local RAM
• speed

It can happen that same brand and same model GPUs don't all get used at the same time, that's then usually due to a mismatch in one of the above criteria.

BOINC can be instructed to use all GPUs it finds, if they aren't used by default. This is done via the client configuration file, cc_config.xml which by default lives in the BOINC data directory.